This occurs when you are trying to replace with a different PDF Version of the file. Download the file you are trying to replace and inspect its properties to discover the PDF version. Then inspect the properties of the new PDF file and if the PDF Version is different, you will need to resave in the original files PDF Version.
It may be related to the fact that the files were created with different versions of InDesign and/or that the PDF Producer is different. Marketo categorized the Type of some of our uploaded PDF files as "application/pdf" and some as "application/octet-stream" (screen shot below). You can check to see how Marketo is categorizing the Type of your replacement file by uploading it to Marketo under a different name. If it is a different type, then you need to save the replacement file using the same version of InDesign and/or PDF Producer, so that it will be categorized by Marketo as the same Type as the original file.
Sorry, pushed best answer instead of post!
Thanks again for the info. Looks like I am out of luck on this one since I do not have an older version of InDesign, so I cannot save it using an older version.
Very strange that Marketo would handle files this way since Adobe comes out with new software at least once a year.
I will delete all the old ones and re-upload.